Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_6527
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6823
ACGTcount: A:0.21, C:0.28, G:0.30, T:0.21
Found at i:3947 original size:169 final size:172
Alignment explanation
Indices: 3612--3954 Score: 470
Period size: 169 Copynumber: 2.0 Consensus size: 172
3602 GTAAGGAGTT
3612 AGTTAAACACTTGGCCTGCCGCCCCCGGAGAAATGGCACAACGGGGGCCGTGGTGGTGCGGTGCG
1 AGTTAAACACTTGGCCTGCCGCCCCCGGAGAAATGGCACAACGGGGGCC--GGTGGTGCGGTGCG
* * *
3677 AGCTCCCAACTGTTGGTGGTCCGGGCACTTGTTCAATTTTCTGCCGTGCCGTGCCGTGCCATACT
64 AGCTCCCAACTGTTGGTGGTCCGGGCACTTGTTCAATTTTCTACCG-GCCAT-CCATGCCATACT
*
3742 TCATTCGCCTCTTGTATTTGTTTTGGGCCAACAGAAAAAATTTCTA
127 TCATTCGCCTCTTGTATTTCTTTTGGGCCAACAGAAAAAATTTCTA
3788 AGTTAAACACTTGGCCGTGCCGCCCCCTCGGA-AACATGGCACAACGGGGG-C-GTGGTGCGAGT
1 AGTTAAACACTTGGCC-TGCCG-CCCC-CGGAGAA-ATGGCACAACGGGGGCCGGTGGTGCG-GT
*
3850 GCGAGCT-CCAACTGTTGGTGG-CC-GGCACTTGTTCAA-TTTCTACC-GCCAT-CATGCCATAT
61 GCGAGCTCCCAACTGTTGGTGGTCCGGGCACTTGTTCAATTTTCTACCGGCCATCCATGCCATAC
* *
3909 TTCATTCGGCTTCTTGTATTTCTTTTGGGCCAACAGAAAAATTTTC
126 TTCATTC-GCCTCTTGTATTTCTTTTGGGCCAACAGAAAAAATTTC
3955 AATTAATACA
Statistics
Matches: 154, Mismatches: 7, Indels: 19
0.86 0.04 0.11
Matches are distributed among these distances:
168 15 0.10
169 35 0.23
170 4 0.03
172 7 0.05
173 13 0.08
174 2 0.01
175 22 0.14
176 25 0.16
177 5 0.03
178 7 0.05
179 19 0.12
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.28
Consensus pattern (172 bp):
AGTTAAACACTTGGCCTGCCGCCCCCGGAGAAATGGCACAACGGGGGCCGGTGGTGCGGTGCGAG
CTCCCAACTGTTGGTGGTCCGGGCACTTGTTCAATTTTCTACCGGCCATCCATGCCATACTTCAT
TCGCCTCTTGTATTTCTTTTGGGCCAACAGAAAAAATTTCTA
Found at i:5365 original size:42 final size:42
Alignment explanation
Indices: 5006--6003 Score: 1047
Period size: 42 Copynumber: 24.7 Consensus size: 42
4996 CTTGGTTGCA
5006 GGAGCCTCGGACACCATC-GCAACCTAGGGCCCTT-G-C-TGCG
1 GGAGCCTCGG-CACCATCGGCAACCTA-GGCCCTTGGTCGTGCG
*
5046 GGAGCCTCGGCACCAT-TG-AACCT-GG-CCTTGGTCGT-CG
1 GGAGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCG
*
5083 GGAGCCTCGGGC-CCATCGGCAACCTAGGCCC-TGGTCGTTC-
1 GGAGCCTC-GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCG
* *
5123 GG-GCCTCAGAACACCATCGG-AACCTA-GCCCCTGGTC-T-CG
1 GGAGCCTC-G-GCACCATCGGCAACCTAGGCCCTTGGTCGTGCG
*
5162 GGAGCCTCGGCACCATCCGCAACCTAGGCCCTTGGTCGTGCCG
1 GGAGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTCGTG-CG
* *
5205 GGAG-CTC-G-ACCATCGGCAACC-AAG-CC-TGGTCGT-AG
1 GGAGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCG
* *
5240 GGAGCCTCGG-ACCATCGGC-ACC-AGCCCCTTTGTCGT--G
1 GGAGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCG
* *
5277 AGAGCCTCGGCACCATCCGCAACCTAGGCCCTTGGTCGTGCG
1 GGAGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCG
*
5319 GGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGGTCGTAC-
1 GGAGCCTCGG-CACCATCGGCAACCTAGGCCCTTGGTCGTGCG
*
5361 GGAGCCTCGGACACCATCGGC-ACCTAGG-CCTTGGT-GTACG
1 GGAGCCTCGG-CACCATCGGCAACCTAGGCCCTTGGTCGTGCG
5401 GGAGCCTCGGACACCATCGGCAACCTAGGCCC-TGGT-GTGC-
1 GGAGCCTCGG-CACCATCGGCAACCTAGGCCCTTGGTCGTGCG
5441 GGAGCCTC-G-ACCATCGGCAACCTAGGCCC-TGGTCGTGCG
1 GGAGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCG
*
5480 GGAGCCTCGGCACCATCGGCAACCTAGGCCCCTGGTCGTGC-
1 GGAGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCG
*
5521 GGAGCCTCGGCACCATCGGCAACCTAGGCCCCTGGTCGTGC-
1 GGAGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCG
*
5562 GGAGCCTCGGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCG
1 GGAGCCTC-GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCG
*
5605 GGAGCCTCGGGCA-CATC-G-AACCTAGGCCCCTGGTCGTGCG
1 GGAGCCTC-GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCG
* *
5645 GGATCCTCGGGCACCATCGGCAACCTAGGCCCCTGG--GTGC-
1 GGAGCCTC-GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCG
5685 -GAGCCTCGGGCACCATCGGC-ACCTAGGCCC-TGGTCGTGCG
1 GGAGCCTC-GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCG
5725 GGAGCCTCGGGCACCATCGGCAACCTAGGCCC-TGGTCGTGCG
1 GGAGCCTC-GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCG
** ** *
5767 GGAGCCTCGG-ACCAT-GGC-ACCTTCGTGCTTGGAT-GTACG
1 GGAGCCTCGGCACCATCGGCAACCTAGGCCCTTGG-TCGTGCG
5806 GGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGGTCGTGC-
1 GGAGCCTCGG-CACCATCGGCAACCTAGGCCCTTGGTCGTGCG
* *
5848 GGAGCCTCGGGCACCATCGGTAACCTAGGCCCTTGGTCATGCG
1 GGAGCCTC-GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCG
* * *
5891 GGAGCCTGGGCACCATCGGC-ACCT-TGCTGCCTCGGAT-GTGCG
1 GGAGCCTCGGCACCATCGGCAACCTAGGC--CCTTGG-TCGTGCG
* * * **
5933 GGAGCCTCGAGCAGCATTGGC-ACCTTGGTGCTTGGAT-GTGCG
1 GGAGCCTCG-GCACCATCGGCAACCTAGGCCCTTGG-TCGTGCG
*
5975 GGAGCCTCGGACACCATAGGCAACCTAGG
1 GGAGCCTCGG-CACCATCGGCAACCTAGG
6004 ACGTTGGATG
Statistics
Matches: 845, Mismatches: 49, Indels: 125
0.83 0.05 0.12
Matches are distributed among these distances:
35 9 0.01
36 10 0.01
37 71 0.08
38 55 0.07
39 93 0.11
40 150 0.18
41 143 0.17
42 208 0.25
43 105 0.12
44 1 0.00
ACGTcount: A:0.16, C:0.35, G:0.32, T:0.17
Consensus pattern (42 bp):
GGAGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCG
Found at i:5560 original size:244 final size:246
Alignment explanation
Indices: 5006--6003 Score: 1126
Period size: 244 Copynumber: 4.1 Consensus size: 246
4996 CTTGGTTGCA
* * *
5006 GGAGCCTCGGACACCATC-GCAACCTAGGGCCCTTG-C-TGCGGGAGCCTCGGCACCATTG-AAC
1 GGAGCCTCGG-CACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGCACCATGGCAAC
* *
5067 CT-GG-CCTTGGTCGT-CGGGAGCCTCGGGC-CCATCGGCAACCTAGGCCC-TGGTCGTTCGG-G
65 CTAGGCCCTTGGTCGTGCGGGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGGTCGTGCGGAG
* *
5126 CCTCAGAACACCATCGGAACCTA-GCCCCTGGTC-T-CGGGAGCCTC-GGCACCATCCGCAACCT
130 CCTC-GGACACCATCGGAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCT
* *
5187 AGGCCCTTGGTCGTGCCGGGAG-CTCGACCATCGGCAACC-AAG-CCTGGTCGT-AG
194 AGGCCC-TGGT-GTG-CGGGAGCCTCGACCATCGGC-ACCTAGGCCCTGGTCGTGCG
* * *
5240 GGAGCCTCGG-ACCATCGGC-ACC-A-GCCCCTTTGTCGT--GAGAGCCTCGGCACCATCCGCAA
1 GGAGCCTCGGCACCATCGGCAACCTAGGCCCC-TGGTCGTGCGGGAGCCTCGGCACCAT-GGCAA
*
5299 CCTAGGCCCTTGGTCGTGCGGGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGGTCGTACGGA
64 CCTAGGCCCTTGGTCGTGCGGGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGGTCGTGCGGA
* * * *
5364 GCCTCGGACACCATCGGCACCTAGG-CCTTGGT-GTACGGGAGCCTCGGACACCATCGGCAACCT
129 GCCTCGGACACCATCGGAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCT
5427 AGGCCCTGGTGTGC-GGAGCCTCGACCATCGGCAACCTAGGCCCTGGTCGTGCG
194 AGGCCCTGGTGTGCGGGAGCCTCGACCATCGGC-ACCTAGGCCCTGGTCGTGCG
5480 GGAGCCTCGGCACCATCGGCAACCTAGGCCCCTGGTCGTGC-GGAGCCTCGGCACCATCGGCAAC
1 GGAGCCTCGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGCACCAT-GGCAAC
* * *
5544 CTAGGCCCCTGGTCGTGC-GGAGCCTCGGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGA
65 CTAGGCCCTTGGTCGTGCGGGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGGTCGTGC-GGA
* *
5608 GCCTCGGGCA-CATC-GAACCTAGGCCCCTGGTCGTGCGGGATCCTCGGGCACCATCGGCAACCT
129 GCCTCGGACACCATCGGAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCT
5671 AGGCCCCTGG-GTGC--GAGCCTCGGGCACCATCGGCACCTAGGCCCTGGTCGTGCG
194 AGG-CCCTGGTGTGCGGGAGCCTC--G-ACCATCGGCACCTAGGCCCTGGTCGTGCG
5725 GGAGCCTCGGGCACCATCGGCAACCTAGG-CCCTGGTCGTGCGGGAGCCTCGG-ACCATGGC-AC
1 GGAGCCTC-GGCACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGCACCATGGCAAC
** ** *
5787 CTTCGTGCTTGGAT-GTACGGGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGGTCGTGCGGA
65 CTAGGCCCTTGG-TCGTGCGGGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGGTCGTGCGGA
* * *
5851 GCCTCGGGCACCATCGGTAACCTAGGCCCTTGGTCATGCGGGAGCCT-GGGCACCATCGGC-ACC
129 GCCTCGGACACCATCGG-AACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* * * * *
5914 T-TGCTGCCTCGGATGTGCGGGAGCCTCGAGCAGCATTGGCACCTTGGTGCTTGGAT-GTGCG
193 TAGGC--CCT-GG-TGTGCGGGAGCCTCGA-C--CATCGGCACCTAGG-CCCTGG-TCGTGCG
*
5975 GGAGCCTCGGACACCATAGGCAACCTAGG
1 GGAGCCTCGG-CACCATCGGCAACCTAGG
6004 ACGTTGGATG
Statistics
Matches: 669, Mismatches: 42, Indels: 90
0.84 0.05 0.11
Matches are distributed among these distances:
230 4 0.01
231 20 0.03
232 11 0.02
233 8 0.01
234 12 0.02
235 10 0.01
236 17 0.03
237 37 0.06
238 38 0.06
239 29 0.04
240 32 0.05
241 9 0.01
242 12 0.02
243 89 0.13
244 145 0.22
245 68 0.10
246 66 0.10
247 6 0.01
249 21 0.03
250 34 0.05
251 1 0.00
ACGTcount: A:0.16, C:0.35, G:0.32, T:0.17
Consensus pattern (246 bp):
GGAGCCTCGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGCACCATGGCAACC
TAGGCCCTTGGTCGTGCGGGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGGTCGTGCGGAGC
CTCGGACACCATCGGAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAG
GCCCTGGTGTGCGGGAGCCTCGACCATCGGCACCTAGGCCCTGGTCGTGCG
Found at i:5823 original size:286 final size:284
Alignment explanation
Indices: 5006--5908 Score: 1114
Period size: 286 Copynumber: 3.2 Consensus size: 284
4996 CTTGGTTGCA
* * * *
5006 GGAGCCTCGGACACCATC-GCAACCTAGGGCCCTTG-C-TGCGGGAGCCTC-GGCACCATTGAAC
1 GGAGCCTCGGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGAAC
* *
5067 CT-GG-CCTTGGTCGTCGGGAGCCTCGGGC-CCATCGGCAACCTAGGCCCTGGTCGTTCGGGCCT
66 CTAGGCCCTTGGTCGTCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTGGT-GTGCGAGCCT
* * * *
5129 CAGAACACCATCGGAACCTAGCCCCTGGTC-T-CGGGAGCCTCGGCACCATCCGCAACCTAGGCC
130 C-GGACACCATCGGCACCTAGGCCCTGGTCGTGCGGGAGCCTCGGCACCATCGGCAACCTAGGCC
* *
5192 CTTGGTCGTGCCGGGAG-CTC-GACCATCGGCAAC-CAAGCCTGGTCGTA-GGGAGCCTCGG-AC
194 C-TGGTCGTG-CGGGAGCCTCGGACCATCGGCACCTCGAGCCTGGTCGTACGGGAGCCTCGGCAC
*
5252 CATCGGC-ACC-A-GCCCCTTTGTCGTG-
257 CATCGGCAACCTAGGCCCC-TGGTCGTGC
* * * *
5277 AGAGCCTC-GGCACCATCCGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGACACCATCGGCA
1 GGAGCCTCGGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATC-G-A
* * *
5341 ACCTAGGCCCTTGGTCGTAC-GGAGCCTCGGACACCATCGGC-ACCTAGGCCTTGGTGTACGGGA
64 ACCTAGGCCCTTGGTCGT-CGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTGGTGT--GCGA
5404 GCCTCGGACACCATCGGCAACCTAGGCCCTGGT-GTGC-GGAGCCTC-G-ACCATCGGCAACCTA
126 GCCTCGGACACCATCGGC-ACCTAGGCCCTGGTCGTGCGGGAGCCTCGGCACCATCGGCAACCTA
* *
5465 GGCCCTGGTCGTGCGGGAGCCTCGGCACCATCGGCAACCTAG-GCCCCTGGTCGTGC-GGAGCCT
190 GGCCCTGGTCGTGCGGGAGCCTCGG-ACCATCGGC-ACCTCGAG--CCTGGTCGTACGGGAGCCT
5528 CGGCACCATCGGCAACCTAGGCCCCTGGTCGTGC
251 CGGCACCATCGGCAACCTAGGCCCCTGGTCGTGC
5562 GGAGCCTCGGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCA-CATCGAAC
1 GGAGCCTCGGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGAAC
* *
5626 CTAGGCCCCTGGTCGTGCGGGATCCTCGGGCACCATCGGCAACCTAGGCCCCTGG-GTGCGAGCC
66 CTAGGCCCTTGGTCGT-CGGGAGCCTCGGGCACCATCGGCAACCTAGG-CCCTGGTGTGCGAGCC
*
5690 TCGGGCACCATCGGCACCTAGGCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGC
129 TCGGACACCATCGGCACCTAGGCCCTGGTCGTGCGGGAGCCTC-GGCACCATCGGCAACCTAGGC
* *
5755 CCTGGTCGTGCGGGAGCCTCGGACCAT-GGCACCTTCGTGCTTGGAT-GTACGGGAGCCTCGGAC
193 CCTGGTCGTGCGGGAGCCTCGGACCATCGGCACC-TCGAGCCTGG-TCGTACGGGAGCCTCGG-C
*
5818 ACCATCGGCAACCTAGGCCCTTGGTCGTGC
255 ACCATCGGCAACCTAGGCCCCTGGTCGTGC
* * *
5848 GGAGCCTCGGGCACCATCGGTAACCTAGGCCCTTGGTCATGCGGGAGCCT-GGGCACCATCG
1 GGAGCCTCGGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCG
5909 GCACCTTGCT
Statistics
Matches: 550, Mismatches: 39, Indels: 71
0.83 0.06 0.11
Matches are distributed among these distances:
270 8 0.01
271 21 0.04
272 1 0.00
273 12 0.02
274 7 0.01
275 7 0.01
276 16 0.03
277 24 0.04
278 55 0.10
279 40 0.07
280 1 0.00
281 19 0.03
282 23 0.04
283 46 0.08
284 46 0.08
285 46 0.08
286 138 0.25
287 40 0.07
ACGTcount: A:0.16, C:0.36, G:0.32, T:0.16
Consensus pattern (284 bp):
GGAGCCTCGGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGAAC
CTAGGCCCTTGGTCGTCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTGGTGTGCGAGCCTC
GGACACCATCGGCACCTAGGCCCTGGTCGTGCGGGAGCCTCGGCACCATCGGCAACCTAGGCCCT
GGTCGTGCGGGAGCCTCGGACCATCGGCACCTCGAGCCTGGTCGTACGGGAGCCTCGGCACCATC
GGCAACCTAGGCCCCTGGTCGTGC
Found at i:6046 original size:286 final size:284
Alignment explanation
Indices: 5006--6035 Score: 1017
Period size: 286 Copynumber: 3.6 Consensus size: 284
4996 CTTGGTTGCA
* * *
5006 GGAGCCTCGGACACCATC-GCAACCTAGGGCCCTT-G-C-TGCGGGAGCCTC-GGCACCAT-TGA
1 GGAGCCTCGGGCACCATCGGCAACCTA-GGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC
* * *
5065 ACCT-GGCCTTGGTCGT-CGGGAGCCTCGGGC-CCATCGGCAACCTAGGCCCTGGTCGTTC-GG-
65 ACCTAGGCCTCGGTCGTGCGGGAGCCTC-GGCACCATCGGC-ACCTAGGCCTTGGT-GTGCGGGA
* * * *
5125 GCCTCAGAACACCATCGG-AACCTAGCCCCTGGTCT-CGGGAGCCTCG-GCACCATCCGCAACCT
127 GCCTC-GGACACCATCGGCAACCTAGGCCCTGGTGTGC-GGAGCCTCGAGCACCA---GGAACCT
*
5187 AGGCCCTTGGTCGTGCCGGGAG-CTC-G-ACCATCGGCAACC-AAG--CCTGGTCGTA-GGGAGC
187 A-GCCC-TGGTCGTG-CGGGAGCCTCGGCACCATCGGCAACCTACGCCCCTGGTCGTACGGGAGC
* *
5245 CTCGG-ACCATCGGC-ACC-AGCCCCTTTGTCGTG-
249 CTCGGCACCATCGGCAACCTAGGCCCTTGGTCGTGC
* * *
5277 AGAGCCTC-GGCACCATCCGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGACACCATCGGCA
1 GGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-
* * *
5341 ACCTAGGCCCTTGGTCGTAC-GGAGCCTCGGACACCATCGGCACCTAGGCCTTGGTGTACGGGAG
65 ACCTAGG-CCTCGGTCGTGCGGGAGCCTCGG-CACCATCGGCACCTAGGCCTTGGTGTGCGGGAG
* *
5405 CCTCGGACACCATCGGCAACCTAGGCCCTGGTGTGCGGAGCCTCGACCATC-GGCAACCTAGGCC
128 CCTCGGACACCATCGGCAACCTAGGCCCTGGTGTGCGGAGCCTCGAGCACCAGG-AACCTA-GCC
* *
5469 CTGGTCGTGCGGGAGCCTCGGCACCATCGGCAACCTAGGCCCCTGGTCGTGC-GGAGCCTCGGCA
191 CTGGTCGTGCGGGAGCCTCGGCACCATCGGCAACCTACGCCCCTGGTCGTACGGGAGCCTCGGCA
*
5533 CCATCGGCAACCTAGGCCCCTGGTCGTGC
256 CCATCGGCAACCTAGGCCCTTGGTCGTGC
* *
5562 GGAGCCTCGGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCA-CATC-GAA
1 GGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCA
* * *
5625 CCTAGGCCCCTGGTCGTGCGGGATCCTCGGGCACCATCGGCAACCTAGGCCCCTGG-GTGC--GA
66 CCTAGGCCTC-GGTCGTGCGGGAGCCTC-GGCACCATCGGC-ACCTAGG-CCTTGGTGTGCGGGA
* *
5687 GCCTCGGGCACCATCGGC-ACCTAGGCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCT
127 GCCTCGGACACCATCGGCAACCTAGGCCCTGGT-GTGC-GGAGCCTCGAGCACCA--GG-AACCT
* ** *
5751 AGGCCCTGGTCGTGCGGGAGCCTCGG-ACCAT-GGC-ACCTTCGTGCTTGGAT-GTACGGGAGCC
187 A-GCCCTGGTCGTGCGGGAGCCTCGGCACCATCGGCAACCTACGCCCCTGG-TCGTACGGGAGCC
5812 TCGGACACCATCGGCAACCTAGGCCCTTGGTCGTGC
250 TCGG-CACCATCGGCAACCTAGGCCCTTGGTCGTGC
* *
5848 GGAGCCTCGGGCACCATCGGTAACCTAGGCCCTTGGTCATGCGGGAGCCT-GGGCACCATCGGCA
1 GGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCA
* * * * *
5912 CCTTGCTGCCTCGGAT-GTGCGGGAGCCTCGAGCAGCATTGGCACCTTGGTGCTTGGATGTGCGG
66 CCTAG--GCCTCGG-TCGTGCGGGAGCCTCG-GCACCATCGGCACCTAGG-CCTTGG-TGTGCGG
* ** *
5976 GAGCCTCGGACACCATAGGCAACCTAGGACGTTGGATGTGCGGATGCCTCGAGCAGCAGG
125 GAGCCTCGGACACCATCGGCAACCTAGG-CCCTGG-TGTGCGGA-GCCTCGAGCACCAGG
6036 GGCACCCTGG
Statistics
Matches: 643, Mismatches: 59, Indels: 94
0.81 0.07 0.12
Matches are distributed among these distances:
270 15 0.02
271 16 0.02
272 1 0.00
273 12 0.02
274 7 0.01
275 7 0.01
276 16 0.02
277 19 0.03
278 58 0.09
279 40 0.06
280 4 0.01
281 19 0.03
282 25 0.04
283 40 0.06
284 54 0.08
285 42 0.07
286 135 0.21
287 51 0.08
288 23 0.04
289 9 0.01
291 20 0.03
292 10 0.02
293 19 0.03
294 1 0.00
ACGTcount: A:0.16, C:0.35, G:0.33, T:0.17
Consensus pattern (284 bp):
GGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCA
CCTAGGCCTCGGTCGTGCGGGAGCCTCGGCACCATCGGCACCTAGGCCTTGGTGTGCGGGAGCCT
CGGACACCATCGGCAACCTAGGCCCTGGTGTGCGGAGCCTCGAGCACCAGGAACCTAGCCCTGGT
CGTGCGGGAGCCTCGGCACCATCGGCAACCTACGCCCCTGGTCGTACGGGAGCCTCGGCACCATC
GGCAACCTAGGCCCTTGGTCGTGC
Found at i:6047 original size:85 final size:84
Alignment explanation
Indices: 5006--6062 Score: 582
Period size: 83 Copynumber: 13.0 Consensus size: 84
4996 CTTGGTTGCA
5006 GGAGCCTCGGACACCATC-GCAACCTAGGGCCCTT-G-C-TGCGGGAGCCTCG-GCACCATT-G-
1 GGAGCCTCGGACACCATCGGCAACCTA-GG-CCTTGGTCGTGCGGGAGCCTCGAGCACCATTGGC
* *
5064 AACCTGG-CCTTGG-TCGT-CG
64 ACCCTGGTGCTTGGAT-GTGCG
* * * * *
5083 GGAGCCTCGGGC-CCATCGGCAACCTAGGCCCTGGTCGTTC-GG-GCCTCAGAACACCATCGG-A
1 GGAGCCTCGGACACCATCGGCAACCTAGGCCTTGGTCGTGCGGGAGCCTC-GAGCACCATTGGCA
* * ** * *
5144 ACCTAGCCCCTGG-TCT-CG
65 CCCTGGTGCTTGGATGTGCG
* *
5162 GGAGCCTCGG-CACCATCCGCAACCTAGGCCCTTGGTCGTGCCGGGAG-CTC--G-ACCATCGGC
1 GGAGCCTCGGACACCATCGGCAACCTAGG-CCTTGGTCGTG-CGGGAGCCTCGAGCACCATTGGC
* ** * *
5222 AACC--AAGCCTGG-TCGT-AG
64 ACCCTGGTGCTTGGAT-GTGCG
* * * **
5240 GGAGCCTCGG--ACCATCGGC-ACC-AGCCCCTTTGTCGT--GAGAGCCTCG-GCACCATCCGCA
1 GGAGCCTCGGACACCATCGGCAACCTAG-GCCTTGGTCGTGCGGGAGCCTCGAGCACCATTGGCA
* **
5298 ACCTAGGCCCTTGG-TCGTGCG
65 CCCT-GGTGCTTGGAT-GTGCG
* *
5319 GGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGGTCGTAC-GGAGCCTCG-GACACCATCGGC
1 GGAGCCTCGGACACCATCGGCAACCTAGG-CCTTGGTCGTGCGGGAGCCTCGAG-CACCATTGGC
* *
5382 A-CCTAGG-CCTTGG-TGTACG
64 ACCCT-GGTGCTTGGATGTGCG
* * *
5401 GGAGCCTCGGACACCATCGGCAACCTAGGCCCTGGT-GTGC-GGAGCCTC--G-ACCATCGGCAA
1 GGAGCCTCGGACACCATCGGCAACCTAGGCCTTGGTCGTGCGGGAGCCTCGAGCACCATTGGCAC
* *
5461 CCTAGG-CCCTGG-TCGTGCG
66 CCT-GGTGCTTGGAT-GTGCG
* *
5480 GGAGCCTCGG-CACCATCGGCAACCTAGGCCCCTGGTCGTGC-GGAGCCTCG-GCACCATCGGCA
1 GGAGCCTCGGACACCATCGGCAACCTAGG-CCTTGGTCGTGCGGGAGCCTCGAGCACCATTGGCA
* ** *
5542 ACCTAGGCCCCTGG-TCGTGC-
65 CCCT-GGTGCTTGGAT-GTGCG
* * * *
5562 GGAGCCTCGGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCA-CA-TCG-A
1 GGAGCCTCGGACACCATCGGCAACCTAGG-CCTTGGTCGTGCGGGAGCCTCGAGCACCATTGGCA
* ** *
5624 ACCTAGGCCCCTGG-TCGTGCG
65 CCCT-GGTGCTTGGAT-GTGCG
* * * * *
5645 GGATCCTCGGGCACCATCGGCAACCTAGGCCCCTGG--GTGC--GAGCCTCGGGCACCATCGGCA
1 GGAGCCTCGGACACCATCGGCAACCTAGG-CCTTGGTCGTGCGGGAGCCTCGAGCACCATTGGCA
* *
5706 -CCTAGG-CCCTGG-TCGTGCG
65 CCCT-GGTGCTTGGAT-GTGCG
* *
5725 GGAGCCTCGGGCACCATCGGCAACCTAGGCCCTGGTCGTGCGGGAGCCTCG-G-ACCA-TGGCAC
1 GGAGCCTCGGACACCATCGGCAACCTAGGCCTTGGTCGTGCGGGAGCCTCGAGCACCATTGGCAC
* * *
5787 CTTCGTGCTTGGATGTACG
66 CCTGGTGCTTGGATGTGCG
* * *
5806 GGAGCCTCGGACACCATCGGCAACCTAGGCCCTTGGTCGTGC-GGAGCCTCGGGCACCATCGGTA
1 GGAGCCTCGGACACCATCGGCAACCTAGG-CCTTGGTCGTGCGGGAGCCTCGAGCACCATTGGCA
* ** *
5870 ACCTAGGCCCTTGG-TCATGCG
65 CCCT-GGTGCTTGGAT-GTGCG
* * * *
5891 GGAGCCT-GGGCACCATCGGC-ACCTTGCTGCCTCGGAT-GTGCGGGAGCCTCGAGCAGCATTGG
1 GGAGCCTCGGACACCATCGGCAACCTAG--GCCTTGG-TCGTGCGGGAGCCTCGAGCACCATTGG
*
5953 CACCTTGGTGCTTGGATGTGCG
63 CACCCTGGTGCTTGGATGTGCG
* * * **
5975 GGAGCCTCGGACACCATAGGCAACCTAGGACGTTGGAT-GTGC-GGATGCCTCGAGCAGCAGGGG
1 GGAGCCTCGGACACCATCGGCAACCTAGG-CCTTGG-TCGTGCGGGA-GCCTCGAGCACCATTGG
*
6038 CACCCTGGTGCCTCGGATGTGCG
63 CACCCTGGTG-CTTGGATGTGCG
6061 GG
1 GG
6063 CTAAAGAAAG
Statistics
Matches: 832, Mismatches: 80, Indels: 127
0.80 0.08 0.12
Matches are distributed among these distances:
72 4 0.00
73 3 0.00
74 1 0.00
75 26 0.03
76 16 0.02
77 47 0.06
78 67 0.08
79 90 0.11
80 86 0.10
81 83 0.10
82 104 0.12
83 115 0.14
84 75 0.09
85 97 0.12
86 18 0.02
ACGTcount: A:0.16, C:0.35, G:0.33, T:0.17
Consensus pattern (84 bp):
GGAGCCTCGGACACCATCGGCAACCTAGGCCTTGGTCGTGCGGGAGCCTCGAGCACCATTGGCAC
CCTGGTGCTTGGATGTGCG
Found at i:6056 original size:43 final size:43
Alignment explanation
Indices: 5887--6062 Score: 155
Period size: 43 Copynumber: 4.1 Consensus size: 43
5877 CCCTTGGTCA
* * * * *
5887 TGCGGGAGCCT-GGGCACCATCGGCACCTTGCTGCCTCGGATG
1 TGCGGGAGCCTCGAGCAGCATAGGCACCCTGGTGCCTCGGATG
* * *
5929 TGCGGGAGCCTCGAGCAGCATTGGCACCTTGGTG-CTTGGATG
1 TGCGGGAGCCTCGAGCAGCATAGGCACCCTGGTGCCTCGGATG
* * * * *
5971 TGCGGGAGCCTCG-GACACCATAGGCAACCTAGG-ACGTTGGATG
1 TGCGGGAGCCTCGAG-CAGCATAGGCACCCT-GGTGCCTCGGATG
**
6014 TGC-GGATGCCTCGAGCAGCAGGGGCACCCTGGTGCCTCGGATG
1 TGCGGGA-GCCTCGAGCAGCATAGGCACCCTGGTGCCTCGGATG
6057 TGCGGG
1 TGCGGG
6063 CTAAAGAAAG
Statistics
Matches: 108, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
41 1 0.01
42 47 0.44
43 57 0.53
44 3 0.03
ACGTcount: A:0.15, C:0.28, G:0.38, T:0.19
Consensus pattern (43 bp):
TGCGGGAGCCTCGAGCAGCATAGGCACCCTGGTGCCTCGGATG
Done.